The Avengers Initiative
by The Thief of Eddis
Summary: During the events of 'Slash Fiction' Dean and Sam are captured by a government operation and have been in solitary confinement for a year. They are released for one reason only, to help the government with a top priority assignment that enlists the help of not only them, but six other skilled individuals. Rated T for violence, swearing, and the personalities of Dean and Tony.
1. Prologue

**Disclaimer: I do not own Supernatural or the Avengers**

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Dean sat on the cold hard ground, his back against the wall, and his knees drawn to his chest. He pondered the life he'd led. After all, wasn't that what people normally did in prison? Think back on all the pain they'd caused, the lives they'd torn apart? Maybe that wasn't what normal people did, but then again, no one in their right mind would call Dean Winchester normal. He wouldn't be in Ryker's if that were the case.

Sam, no doubt, was in a cell in Alcatraz, his mind slowly deteriorating from the hellish hallucinations he'd been having. The worst part was, Dean couldn't be there to bring him back to reality, to help him out of his nightmares come to life. Dean relished in the fact that Sam didn't know about Amy. He still felt incredibly guilty over it, but at least Sam didn't know. And if Dean did spend the rest of his life in this cell, Sam would never have to know.

Dean sighed, placing his head in his hands. He could faintly remember when the toughest thing he'd had to face was a wendigo. He chuckled, remembering when he thought he couldn't handle a haunted airplane. Little had he known then, he'd have to face hell, an apocalypse, and damn leviathans. Man, he hated those flesh eaters.

It was precisely those monstrosities that led him into this mess. Sure, being framed by a couple of shape shifters beforehand hadn't helped his criminal record, but he'd never been the FBI's most wanted. Which of course, led to S.H.I.E.L.D.'s involvement.

Dean had never heard of the Strategic Homeland Intervention Enforcement and Logistics Division before, but it had quickly become apparent they weren't to be trifled with. All of their agents were highly trained and skilled. From what he'd heard, a few of them were former assassins as well. Dean could deal with freakish hell bound monsters, but humans were another matter entirely.

With a secret organization like S.H.I.E.L.D., Dean knew there was no escaping this claustrophobic cell. It would be easier to escape out Hell's back door. If he wanted out, he'd have to negotiate. And he doubted they'd listen to a convicted murderer like himself.

So, nothing skyrocketed Dean's curiosity like a visit from the director of S.H.I.E.L.D. himself. He was dark skinned and bald, with a goatee, and a black eye patch covering his left eye. He wore a long, dark trench coat, and a leather uniform, accompanied with a gun and holster. He meant business.

The man approached Dean, his footsteps echoing loudly in the quiet space. He looked down upon the Winchester.

"We need to talk."

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**A/N: Thanks for reading the prologue for my new story. I should be posting the first chapter soon.**


	2. Global Catastrophe? Yeah right

Disclaimer: I do not own the Avengers or Supernatural

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The interrogation room was small, and dimly lit. The walls and floors were a dark indigo, with a hexagon pattern imprinted on the surface. In the middle of the room stood a metal table and two chairs, one of which Dean was currently seated on. His wrists were shackled, and an agent stood behind him. Dean wasn't willing to admit it, but he wasn't going anywhere, anytime soon.

The director of S.H.I.E.L.D., Nick Fury, sat in the chair across from him. He placed a file on the table, which Dean assumed was his. Dean couldn't help but notice the worry in the director's expression. But perhaps it was only for show.

Fury made eye contact with Dean, and hesitated. With a small sigh, he opened the file. Dean strained to read the file upside down. He frowned. It didn't have anything to do with him, not that he could tell anyways. There was an image of what Dean would call a cosmic cube. It seemed to be composed of a sort of blue energy, similar to flames. _Right out of a comic book_, Dean thought with a small smirk. Though he couldn't see what he had to do with an object like that.

"We're facing a global catastrophe, Mr. Winchester." The director informed him.

Dean scoffed, unable to help himself. "So were we." He reminded Fury.

"Oh, I almost forgot." The director responded, rolling his one good eye. "Your evil twins, right?" Dean clenched his fists. "You know, I haven't seen them since we took you in."

Of course not, Dick Roman was too cautious for that. No, their operation was probably running smooth as ever. Unless Bobby had figured out a way to stop them. Dean cleared his thoughts. Now was not the time to think about Bobby or Leviathans. Whatever Fury wanted, he had to face head on.

"Wouldn't have expected you to." Dean replied. "It would be a dumbass move on their part."

"Perhaps. Let's put aside this conversation for now, believe it or not, that's not why you're here." The director paused. "We've made some mistakes."

Dean rolled his eyes. "No surprise there."

"An artifact of great importance was stolen a few days ago, and we need help tracking down, and stopping the thief." The director continued.

"What's the big deal?"

"It has the potential to wipe out the planet." The director replied. "We're putting together a team, and you're name came up."

Dean smirked. "Desperate are we?"

"Very."

"Let me guess, the object in question is that cube?" Dean asked, eyeing the file.

The director nodded. "As a matter of fact."

"What's in it for me?"

The director smiled. "A chance to be the hero for once in your life."

Dean scoffed, restraining himself from making a comment he'd only regret. "I'll work under one condition."

The director raised an eyebrow. "And that is?"

"You put Sam on the team too. Believe me, he's an asset."

"Alright, I accept. But both of you will return to your cells when all is well again."

Dean froze, realizing what the director was saying. He and Sam would go right back to solitary confinement, never to see each other again. He couldn't let that happen. Not to Sam. "No."

The director raised an eyebrow. "No?"

"I'll return to that hell hole you call Ryker's, but Sam walks free."

The director was taken aback, and he stared at Dean, no doubt trying to figure him out. "You'll throw away everything for your brother?"

Dean shrugged. "Yeah, well, I guess it's a Winchester thing."

* * *

Hours later, after an alarming flight via quinjet from Ryker's Island, Dean stood waiting on the bridge of S.H.I.E.L.D.'s main base of operations; the helicarrier. Which, to Dean's relief, wasn't in the air. Yet.

He wasn't alone though. Dean doubted the helicarrier was ever completely empty with the number of agents running the day-to-day business of S.H.I.E.L.D. There was one agent, addressed as Agent Morse, whose assignment was to watch his every move. She stood still as a soldier, and reacted to every movement he made, her hand instinctively reaching for the gun at her hip. She didn't have patience for any of his shit either. In fact, she was the reason he'd been unconscious for half of the flight.

"Dean."

Dean froze, recognizing the slightly hoarse voice. He turned slowly and faced his baby brother. "Sammy." He whispered.

The two brothers embraced, and Dean fought the urge to cry. Dammit, he was thirty-three years old for crying out loud. But he couldn't help shed a tear or two. He hadn't seen Sam since the week they were apprehended. While he had been sent to Ryker's, Sam had gone to Alcatraz. The two of them had been apart for so long, but it was all worth it just to see Sammy's smiling face again. Dean smiled, he had his brother back.

Sam pulled away, and grinned. Dean placed a hand on his brother's shoulder. "You ready to save the world, Sammy?"

"Yeah."

The smile slipped off Dean's face as he felt the ground shift beneath them. He watched out the large window as the helicarrier began its ascent into the sky. Sam snickered as Dean clenched his fists and hummed a few notes of Metallica's 'Enter Sandman'.

Sam patted Dean on the back, and chuckled. "Some things never change."

"Gentlemen." Nick Fury greeted, approaching them.

Sam and Dean turned, realizing two other men had joined them. Due to their lack of uniform, Dean assumed they weren't S.H.I.E.L.D. agents. Maybe they were part of the team the director had spoken of.

The one man, a tall blonde in a leather jacket, walked up to Fury and handed him a dollar bill. Dean scoffed. "Lose a bet?"

"None of your concern." Fury responded, eyeing Dean. He threw his hands up in mock surrender.

Sam elbowed his older brother. "Don't push it." He whispered.

"Thank you for coming."

Dean was about to reply with a snarky comment, until he realized the director wasn't speaking to him. He was speaking to the other man. Dean watched the two shake hands.

"Thanks for asking nicely." The man looked around nervously. "So, how long am I staying?"

"Once we get our hands on the tesseract, you're in the wind." The director replied.

"Where are you with that?" The man replied.

"Yeah, where are you with that?" Dean echoed, receiving a glare from the director.

Sam glanced between director Fury and Dean. "Dean." He whispered. "Don't piss him off."

"Might be a bit late for that warning, Sammy."

Sam rolled his eyes. "Yeah, I see that."

"We're sweeping every wirelessly accessible camera on the planet. Cell phones, laptops… If it's connected to a satellite, it's eyes and ears for us." Another agent replied.

"That's still not gonna find them in time."

Dean's head snapped in the direction of the female speaker, and he saw Sam shake his head. She was out of uniform, but the way she held herself, she was obviously another agent. _Man._ Dean thought. _She's hot._

"You have to narrow your field." The second man said. "How many spectrometers do you have access to?"

"How many are there?" The director asked.

"Call every lab you know." The man instructed. "Tell them to put spectrometers on the roof and calibrate them for gamma rays. I'll rough out a tracking algorithm, basic cluster recognition. At least we could rule out a few places. Do you have somewhere for me to work?"

Fury nodded. "Agent Romanoff, could you show Dr. Banner to his laboratory, please?"

Agent Romanoff, the female agent, began leading the second man, Dr. Banner, out. "You're gonna love it, Doc. We got all the toys."

"We done with all the tech stuff now?" Dean questioned. "Cuz I want to know where we come in."

The director grinned. "For now, let's call you plan b. We'll let you know when we require your assistance."

Dean rolled his eyes as the director left. Now, it was just him, Sam, the other agent, and the blonde.

"Alright, so let me get this straight." He said, breaking the silence. "We've got the female agent, the smart doctor, eye patch just left. So, where do you two come in?"

"My name is agent Coulson." Agent Coulson turned to the blonde, a smile lighting up his face. "This here, well, he's a living legend."

Dean scoffed. "A living legend?"

"Yep. Captain Steve Rogers."

Dean furrowed his brow. "Who…"

Sam's eyes widened. "Captain America?"

Coulson nodded. "The one and only."

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A/N: Hope you enjoyed the first chapter! There should be many more to come! Thanks for the reviews, favourites, and follows!


	3. Plan A and Plan B

Disclaimer: I do not own the Avengers/Marvel or Supernatural

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They hadn't heard anything regarding the whereabouts of Loki, or the tesseract, though Agent Coulson and Sam didn't appear to mind. Dean listened to them ramble on, praising the incredible captain, adding multiple adjectives before his name to emphasize his brilliance. Frankly, Dean didn't really give a shit about this so called 'living legend', but the smile that lit up Sam's face made his day. He wasn't about to make it leave.

"And then he sacrificed himself." Sam exclaimed, glancing at Steve, as if challenging him to deny his heroics.

"He was trapped in the ice for over seventy years." Agent Coulson turned to Sam. "I was there while he was unconscious." He boasted, trying to make the six foot four puppy jealous.

Dean sniggered. "Dean, stop it." Sam snapped. Dean threw his hands up in mock surrender.

Dean spared a glance at the two agents assigned to watching him and Sam. They looked utterly bored, and Dean knew they'd rather be in the field or doing important work rather than 'babysitting'. The other agent, Coulson, must have noticed too.

He stood up, and addressed the two agents. "May, Morse, I can take it from here."

"Sir…"

Coulson smiled. "I can handle it. You're relieved."

The agents didn't question Coulson's authority, and were quite eager to leave. The agent turned to Dean and Sam. "Do not make a wrong move, because I will not hesitate to taze you."

"So, who are you? What's your story?" The Captain asked, finally speaking. He glanced between the retreating agents and the siblings.

Dean scoffed. "You want to know our story? Believe me, we could write a book."

Sam chuckled. "If somebody hadn't already done that."

Sam and Dean exchanged a small smile. The Captain and the agent hadn't a clue about the book series based on the hunters' lives. Dean wished those books could just rot in Hell.

Agent Coulson wasn't amused. "Captain, meet Sam and Dean Winchester…"

"Dean and Sam." Dean interrupted. "I'm the oldest, my name should go first." Sam rolled his eyes.

"Anyways, the two of them have been on S.H.I.E.L.D's radar for quite some time. There's quite a list."

Steve raised an eyebrow. "Do I even want to know what's on it?"

"Probably not." Sam admitted.

"Dean is charged with mail fraud, credit card fraud, grave desecrations, breaking and entering, armed robbery, kidnapping, and three counts of first degree murder." The Captain's eyes widened. "Sam is charged as being an accomplice. We thought they had died in a sheriff's station in Monument, Colorado. Turns out we were wrong."

The Captain raised an eyebrow. "You're criminals?"

Dean hesitated. "It's complicated."

"No, it's not." Steve argued. "You killed innocent people."

Dean opened his mouth to respond, but snapped it close. The Captain was right. He'd let so many people down. Sam, Jo, Ellen, Amy… Dean froze at the thought of Amy, and glanced sideways at Sam. His brother still didn't know about that. Dean bit his lip, and choked out. "You're damn right about that."

Dean turned away from the agent and super soldier and slumped into his chair. He heard a whisper from Sam. "Shut up." He turned, concerned, and saw Sam staring at an empty chair, squeezing his left hand. He frowned, he didn't want Sam to suffer, but he didn't want the agent or Captain to know about Sam's condition either. Dean locked eyes with his brother and knew Sam felt the same way.

He turned his attention back to the agent and the Captain, but they seemed to be in a deep discussion about trading cards. Dean chuckled, everybody had a geek side nowadays.

An agent approached the four men. "We got a hit." He said, gaining their attention. "Sixty seven percent match. Weight, crossmatch, seventy nine percent."

"Location?" Agent Coulson asked.

"Stuttgart, Germany. 28, Konigstrasse. He's not exactly hiding."

"Captain, you're up." Dean heard director Fury say behind him.

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"You brought us here to help. And now you won't let us friggin' help!" Dean yelled at the director. Sam stayed silent beside him. The Captain had left to suit up, and Dean was determined to convince the director to let them go too. They sure as hell weren't going to sit on their asses.

"You're more plan B." The director responded, his patience wearing thin.

"Crappy idea to have plan A in Germany and plan B on the helicarrier. Quite a bit of travel distance for backup." Dean pointed out.

The director sighed. "Coulson, will you escort the Winchesters to Dr. Banner's laboratory. Perhaps they can be of assistance. At the very least they can keep each other busy. Have Morse guard the entrance." The director turned to Sam and Dean. "Any trouble and she will have orders to shoot, got that?"

Sam nodded. "Loud and clear."

* * *

Sam and Dean were lead into a spacious, high tech laboratory. It was empty, with the exception of one person. The doctor from before, Dr. Banner. He looked up from his work as the brothers entered.

"How's the, uh, UV tracking?" Dean asked.

The doctor raised an eyebrow, clearly amused. "You mean Gamma?"

"That's what I said." Dean replied, masking his embarrassment. Sam was the book type, not him.

"As you probably know, we got a hit on Loki's whereabouts, now all we do is wait for them to bring him in." The doctor sighed. "The sooner this fiasco is over, the sooner I can leave."

"Not a big S.H.I.E.L.D. person, huh?" Sam asked.

"You could say that."

Dean took a seat in one of the chairs and propped his feet up on the counter. "Well, guess that's something we have in common."

The doctor frowned. "Aren't the two of you agents?"

Dean scoffed. "If we were, there wouldn't be an agent posted at the entrance."

"Then who are you?"

"I'm Dean, that's my brother Sam." Dean introduced. "We're criminals, according to S.H.I.E.L.D. Tell me doctor, why hate the secret spy organization?"

"Let's just say I have a severe case of multi-personality disorder. They're not too fond of the other guy."

"I see…"

Doctor Banner held out his hand. "I'm Bruce by the way. Doctor Bruce Banner."

"Nice to meet you, Bruce." Sam replied, shaking the man's hand. Dean did too.

Bruce glanced at the agents posted at the door. "I guess the three of us, in a way, are in the same boat."

"Guess so."

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A/N: Sorry for the wait, I had the general outline of the chapter, just never got around to filling in the blanks. The next chapter should introduce the rest of the Avengers (except maybe Clint, for obvious reasons). I don't think I put enough of Sam's hallucinations, so I'll try to incorporate that more in future chapters. Thanks for the reviews, favorites and follows!


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